I'm not really sure what you're looking for here...you can get 10 different replies with 10 different setups. There is no single solution. Do some in shop research and go with what your ears tell you
Fwiw, I went pretty basic and it still blows the stock system away by a long shot. Sony Xplod HU(50 watts x 4) and Xplod amp(250 watts mono). The head unit powers 4 infinity 3 way "subs" in the dash and doors (5" iirc), and the amp powers a 8" kicker sub. Way more sound than I need and it sounds amazing at 75mph with the top down.
As far as your rear deck box, there are lots of threads about replacement speakers.